# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 02:11:53 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 3-[(3,4-dichlorobenzyl)sulfanyl]thiophene-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1sccc1SCc2ccc(Cl)c(Cl)c2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 NXY  NXY  '3-[(3,4-dichlorobenzyl)sulfanyl]thiophene-2-carboxylic acid'  ligand  25  18  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NXY
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 NXY  C1    C   CR5    0  -0.029  -2.6885  -0.5013  -0.0072
 NXY  C2    C   CR5    0  -0.378  -3.8112   0.2845   0.0361
 NXY  S3    S   S2     0   0.076  -1.0820   0.1857  -0.1940
 NXY  C4    C   CR15   0  -0.185  -2.9936  -1.8899   0.1163
 NXY  S5    S   S2     0   0.218  -5.2315  -0.6657   0.2271
 NXY  C6    C   C      0   0.409  -3.9211   1.7702  -0.0555
 NXY  C7    C   CH2    0  -0.659  -0.0415  -1.3150  -0.1701
 NXY  C8    C   CR15   0  -0.467  -4.3306  -2.1165   0.2491
 NXY  O9    O   O      0  -0.582  -2.8417   2.3781  -0.1987
 NXY  O10   O   OC    -1  -0.596  -5.0694   2.2453   0.0201
 NXY  C11   C   CR6    0   0.119   1.3734  -0.8535  -0.3399
 NXY  C12   C   CR16   0  -0.252   2.1557  -0.5718   0.7731
 NXY  C13   C   CR16   0  -0.285   1.9101  -0.6544  -1.6082
 NXY  C14   C   CR6    0   0.022   3.4561  -0.1155   0.6231
 NXY  C15   C   CR16   0  -0.200   3.2073  -0.1973  -1.7635
 NXY  C16   C   CR6    0  -0.016   3.9857   0.0747  -0.6480
 NXY  CL17  CL  CL     0  -0.097   4.4024   0.2092   2.0257
 NXY  CL18  CL  CL     0  -0.097   5.5993   0.6398  -0.8530
 NXY  H4    H   HCR5   0   0.275  -2.2651  -2.6863   0.1100
 NXY  H7    H   HCH2   0   0.291  -0.1629  -1.8447   0.7753
 NXY  H7A   H   HCH2   0   0.292  -0.3240  -1.9854  -0.9824
 NXY  H8    H   HCR5   0   0.294  -4.8177  -3.0733   0.3602
 NXY  H12   H   HCR6   0   0.285   1.7553  -0.7165   1.7683
 NXY  H13   H   HCR6   0   0.271   1.3149  -0.8627  -2.4883
 NXY  H15   H   HCR6   0   0.290   3.6189  -0.0505  -2.7525

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 NXY  C4    C1    aromatic  1.427  0.020  1.427
 NXY  C1    C2    aromatic  1.371  0.020  1.371
 NXY  C1    S3    single    1.757  0.020  1.757
 NXY  S5    C2    aromatic  1.719  0.020  1.719
 NXY  C2    C6    single    1.493  0.020  1.493
 NXY  C7    S3    single    1.826  0.020  1.826
 NXY  C8    C4    aromatic  1.363  0.020  1.363
 NXY  C4    H4    single    0.930  0.020  1.080
 NXY  C8    S5    aromatic  1.708  0.020  1.708
 NXY  C6    O9    deloc     1.247  0.020  1.247
 NXY  C6    O10   deloc     1.245  0.020  1.245
 NXY  C7    C11   single    1.498  0.020  1.498
 NXY  C7    H7    single    0.970  0.020  1.090
 NXY  C7    H7A   single    0.970  0.020  1.090
 NXY  C8    H8    single    0.930  0.020  1.080
 NXY  C11   C12   aromatic  1.389  0.020  1.389
 NXY  C11   C13   aromatic  1.392  0.020  1.392
 NXY  C12   C14   aromatic  1.386  0.020  1.386
 NXY  C12   H12   single    0.930  0.020  1.080
 NXY  C13   C15   aromatic  1.384  0.020  1.384
 NXY  C13   H13   single    0.930  0.020  1.080
 NXY  CL17  C14   single    1.723  0.020  1.723
 NXY  C14   C16   aromatic  1.390  0.020  1.390
 NXY  C15   C16   aromatic  1.387  0.020  1.387
 NXY  C15   H15   single    0.930  0.020  1.080
 NXY  C16   CL18  single    1.722  0.020  1.722

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 NXY  C4    C1   S3   125.81  3.000
 NXY  S3    C1   C2   121.87  3.000
 NXY  C4    C1   C2   112.33  3.000
 NXY  C6    C2   S5   119.74  3.000
 NXY  C6    C2   C1   128.97  3.000
 NXY  S5    C2   C1   111.29  3.000
 NXY  C7    S3   C1   101.44  3.000
 NXY  H4    C4   C8   122.69  3.000
 NXY  H4    C4   C1   124.97  3.000
 NXY  C8    C4   C1   112.33  3.000
 NXY  C8    S5   C2    92.01  3.000
 NXY  O10   C6   O9   128.26  3.000
 NXY  O10   C6   C2   116.36  3.000
 NXY  O9    C6   C2   115.38  3.000
 NXY  H7A   C7   H7   108.56  3.000
 NXY  H7A   C7   C11  110.47  3.000
 NXY  H7    C7   C11  110.68  3.000
 NXY  H7A   C7   S3   110.35  3.000
 NXY  H7    C7   S3   110.31  3.000
 NXY  C11   C7   S3   106.47  3.000
 NXY  H8    C8   S5   121.08  3.000
 NXY  H8    C8   C4   126.89  3.000
 NXY  S5    C8   C4   112.03  3.000
 NXY  C13   C11  C12  118.95  3.000
 NXY  C13   C11  C7   120.77  3.000
 NXY  C12   C11  C7   120.24  3.000
 NXY  H12   C12  C14  119.37  3.000
 NXY  H12   C12  C11  120.08  3.000
 NXY  C14   C12  C11  120.55  3.000
 NXY  H13   C13  C15  119.18  3.000
 NXY  H13   C13  C11  120.10  3.000
 NXY  C15   C13  C11  120.72  3.000
 NXY  CL17  C14  C16  120.62  3.000
 NXY  C16   C14  C12  120.09  3.000
 NXY  CL17  C14  C12  119.29  3.000
 NXY  H15   C15  C16  119.69  3.000
 NXY  H15   C15  C13  120.28  3.000
 NXY  C16   C15  C13  120.03  3.000
 NXY  CL18  C16  C15  119.64  3.000
 NXY  CL18  C16  C14  120.72  3.000
 NXY  C15   C16  C14  119.65  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 NXY  CONST_01  S5    C8   C4   C1     0.00   0.0  0
 NXY  CONST_02  C8    S5   C2   C1     0.00   0.0  0
 NXY  CONST_03  C8    C4   C1   C2     0.00   0.0  0
 NXY  CONST_04  C4    C8   S5   C2     0.00   0.0  0
 NXY  CONST_05  S5    C2   C1   C4     0.00   0.0  0
 NXY  CONST_06  C16   C14  C12  C11    0.00   0.0  0
 NXY  CONST_07  C16   C15  C13  C11    0.00   0.0  0
 NXY  CONST_08  C15   C13  C11  C12    0.00   0.0  0
 NXY  CONST_09  C15   C16  C14  C12    0.00   0.0  0
 NXY  CONST_10  C14   C12  C11  C13    0.00   0.0  0
 NXY  CONST_11  C14   C16  C15  C13    0.00   0.0  0
 NXY  CONST_12  C8    C4   C1   S3   180.00   0.0  0
 NXY  CONST_13  S5    C2   C1   S3   180.00   0.0  0
 NXY  CONST_14  C6    C2   C1   C4   180.00   0.0  0
 NXY  CONST_15  C8    S5   C2   C6   180.00   0.0  0
 NXY  CONST_16  C14   C12  C11  C7   180.00   0.0  0
 NXY  CONST_17  C15   C13  C11  C7   180.00   0.0  0
 NXY  CONST_18  CL17  C14  C12  C11  180.00   0.0  0
 NXY  CONST_19  CL18  C16  C14  C12  180.00   0.0  0
 NXY  CONST_20  CL18  C16  C15  C13  180.00   0.0  0
 NXY  CONST_21  CL17  C14  C16  C15  180.00   0.0  0
 NXY  CONST_22  H8    C8   C4   C1   180.00   0.0  0
 NXY  CONST_23  H4    C4   C1   C2   180.00   0.0  0
 NXY  CONST_24  H15   C15  C13  C11  180.00   0.0  0
 NXY  CONST_25  H13   C13  C11  C12  180.00   0.0  0
 NXY  CONST_26  H12   C12  C11  C13  180.00   0.0  0
 NXY  Var_01    O9    C6   C2   C1     0.44  30.0  2
 NXY  Var_02    C11   C7   S3   C1   179.37  30.0  1
 NXY  Var_03    C12   C11  C7   S3    91.52  30.0  2

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 NXY  plan-1  C1    0.020
 NXY  plan-1  C2    0.020
 NXY  plan-1  S3    0.020
 NXY  plan-1  C4    0.020
 NXY  plan-1  S5    0.020
 NXY  plan-1  C6    0.020
 NXY  plan-1  C8    0.020
 NXY  plan-1  H4    0.020
 NXY  plan-1  H8    0.020
 NXY  plan-2  C7    0.020
 NXY  plan-2  C11   0.020
 NXY  plan-2  C12   0.020
 NXY  plan-2  C13   0.020
 NXY  plan-2  C14   0.020
 NXY  plan-2  C15   0.020
 NXY  plan-2  C16   0.020
 NXY  plan-2  CL17  0.020
 NXY  plan-2  CL18  0.020
 NXY  plan-2  H12   0.020
 NXY  plan-2  H13   0.020
 NXY  plan-2  H15   0.020
 NXY  plan-3  C2    0.020
 NXY  plan-3  C6    0.020
 NXY  plan-3  O9    0.020
 NXY  plan-3  O10   0.020

